[BioC] where to find a list of housekeeping genes for Affy array (Gene 1.0 ST)

[Robert Castelo]

hi,

if you're searching from something readily available in R, you can try 
to do following:

library(BiocInstaller) ## assuming you installed some BioC package once
biocLite("tweeDEseqCountData")

library(tweeDEseqCountData)
data(hkGenes)
length(hkGenes)
[1] 669
head(hkGenes)
[1] "ENSG00000149925" "ENSG00000102144" "ENSG00000142676" "ENSG00000108298"
[5] "ENSG00000144713" "ENSG00000075624"

check out the help page of 'hkGenes' for the source publication of this 
list.

as you see, these are Ensmbl gene identifiers, but if you need Affy IDs 
from a particular Affy chip, let's say HG-U133 Plus 2.0, you can use the 
great identifier mapping functionality of the package GSEABase, which in 
principle is designed to map identifier between gene sets and 
ExpressionSet objects, but which you can tweak to do this job for you 
passing the housekeeping gene list as if it were one gene set:

library(GSEABase)

dummygs <- GeneSet(hkGenes, geneIdType=ENSEMBLIdentifier())

hkGenesHGU133plus2AffyIDs <- geneIds(mapIdentifiers(dummygs, 
AnnoOrEntrezIdentifier("hgu133plus2")))

length(hkGenesHGU133plus2AffyIDs)
[1] 1263

head(hkGenesHGU133plus2AffyIDs)
[1] "200966_x_at" "214687_x_at" "238996_x_at" "1558365_at"  "200737_at"
[6] "200738_s_at"


cheers,
robert.


On 04/18/2013 02:03 AM, Jack Luo wrote:
> Not sure whether it's an appropriate question for Bioconductor. Is there a
> place to find a list of housekeeping genes (identified by Affy)?
>
> Thanks,
>
> -Jack
>
> 	[[alternative HTML version deleted]]
>
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-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550